Hi Edward.
As you may are aware, I am trying to reproduce parameters from the
article of Kjaergaard et al. http://dx.doi.org/10.1021/bi4001062
In this article, the R1 rate was fitted in the model of DPL94.
At the moment, I am reading in the R1 fitted values from this article, to
be used at relax R1 values.
I have a little trouble to reach the same fitted parameters, and my first
idea is to produce graphs, which will convince me that my input values
are correct.
Whether or not this implementation is good, I have a little trouble
figuring out.
I have now spent around 2 weeks, just to produce graphs, and implementing
the TSMFK01 model took me around 3 weeks?
So spending my time is really an issue here.
The smallest implementation, would be implementing a DPL94 model where
R1 is also fitted.
By adding R1fit as a parameter in relax and write a new target function.
I have no goal to implement this for other models.
Whether or not this model should be available as a standard model in
the GUI is up for discussion.
I think I would have to return to this issue after producing graphs,
running a global fit for the
15 residues, inspect results, double check input values and units
before considering this issue again.
I do think that relax should raise an Error rather than Warning, when
no R1 data is loaded in.
The warning message is lost in the long logfile, and setting the R1
value to 0, is dangerous.
One could consider the two possibilities for the missing of reading R1 values.
Either relax should change to the model, where R1 is fitted of the
user should actively
chose the model where R1 is fitted.
I prefer the last option.
Best
Troels
2014-03-13 11:08 GMT+01:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
Hi Troels,
Are you still interested in implementing the optimisation of the R1
relaxation rate for the R1rho dispersion models? If so, we should
probably discuss and plan how this would be best implemented here on
the mailing list. For example what new user functions should be added
(a user should explicitly turn on such a feature as it is much more
preferable to measure R1), how the data and parameters should be
handled, what types of checks should be added, how the target function
code should be modified, and how to keep the idea compatible with
off-resonance effects in the CPMG-type dispersion models. The whole
concept needs to be carefully designed before any code is written. If
the optimisation of R1 is no longer a goal, then don't worry about
this message.
Regards,
Edward
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Re: Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.